Contacts of the helix formed by residues 305 - 322 (chain B) in PDB entry 3E0D
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 305 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B LEU* 3.6 6.7 - - - +
303B GLY 4.3 0.2 - - - -
304B ARG* 1.3 75.0 - - - +
306B GLU* 1.3 67.3 + - + +
307B ALA* 4.1 11.2 - - + +
308B GLN* 3.3 33.7 + - - +
309B TYR* 3.0 18.7 + - - +
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ILE* 5.6 3.6 - - - +
296B PRO 4.8 1.9 - - - +
297B ARG* 4.6 7.8 - - - +
298B PHE* 3.7 24.8 + - + +
300B LEU* 3.8 18.7 - - + +
304B ARG 3.9 1.0 + - - -
305B THR* 1.3 77.3 - - + +
307B ALA* 1.3 60.6 + - - +
310B LEU 3.6 6.9 + - - -
398B GLY 5.5 1.7 - - - +
400B PRO* 3.3 19.7 - - + +
401B GLY* 3.3 38.3 + - - +
404B LEU* 3.5 22.0 - - + +
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B THR* 3.1 11.0 - - + +
306B GLU* 1.3 78.9 - - - +
308B GLN* 1.3 62.7 + - - +
310B LEU* 3.8 3.0 + - - +
311B ARG* 3.2 27.1 + - - +
391B LEU* 5.5 0.2 - - - +
395B GLU* 3.6 36.5 - - + +
400B PRO* 3.6 18.1 - - + +
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Residues in contact with GLN 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLY 3.5 7.4 + - - +
304B ARG* 3.4 39.2 + - - -
305B THR* 3.2 28.5 + - - +
307B ALA* 1.3 78.2 - - - +
309B TYR* 1.3 59.0 + - - +
311B ARG* 3.2 9.6 - - - +
312B GLU* 2.8 27.3 + - - +
352B GLU 5.4 0.9 - - - -
355B ALA* 3.5 28.3 - - + +
356B ARG* 3.3 35.8 - - - +
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Residues in contact with TYR 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B PHE* 4.3 15.0 - + - -
299B PRO 5.5 1.3 - - - -
300B LEU* 3.8 21.1 - - + -
304B ARG* 4.6 10.5 - - + -
305B THR 3.0 16.4 + - - +
307B ALA 3.4 0.2 - - - -
308B GLN* 1.3 76.0 + - - +
310B LEU* 1.3 58.6 + - - +
312B GLU* 3.2 28.6 + - + +
313B LEU* 2.9 62.2 + - + +
316B LEU* 6.4 1.1 - - + -
404B LEU* 3.3 25.6 - - + -
407B GLN* 5.1 4.4 + - - -
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B GLU 3.6 15.8 + - - +
307B ALA 4.1 3.1 - - - +
308B GLN 3.4 0.4 - - - -
309B TYR* 1.3 77.0 - - - +
311B ARG* 1.3 56.8 + - - +
313B LEU* 3.5 2.8 + - + +
314B THR* 2.7 33.5 + - - +
391B LEU* 4.0 15.7 - - + -
394B ILE* 3.7 23.6 - - + -
395B GLU* 6.1 1.8 - - + -
400B PRO* 3.5 33.7 - - + +
403B PHE* 3.7 27.4 - - + -
404B LEU* 3.8 13.7 - - + +
407B GLN* 6.3 0.7 - - + -
432B VAL* 4.0 16.2 - - + -
436B VAL* 4.5 11.7 - - + -
438B ILE* 6.2 0.9 - - + -
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Residues in contact with ARG 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ALA 3.2 14.9 + - - +
308B GLN* 3.2 10.5 + - - +
310B LEU* 1.3 74.7 - - - +
312B GLU* 1.3 67.1 + - - +
314B THR* 2.9 13.0 + - - -
315B PHE* 3.1 37.9 + - + -
354B LEU 5.0 1.3 - - - -
355B ALA* 3.7 22.1 + - + +
357B VAL 4.3 10.5 + - - -
358B GLU* 5.7 0.2 - - - +
359B GLU* 3.4 33.9 + - - +
362B TRP* 4.7 14.1 - - - +
388B LEU* 4.0 16.0 + - - +
391B LEU* 3.9 40.0 - - + +
392B SER* 4.1 0.8 - - - +
395B GLU* 2.6 31.7 + - - +
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Residues in contact with GLU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ARG* 2.8 52.4 + - - -
308B GLN* 2.8 15.3 + - + +
309B TYR* 3.2 30.6 + - + +
311B ARG* 1.3 72.5 - - - +
313B LEU* 1.3 62.6 + - - +
315B PHE* 3.3 6.1 + - - +
316B LEU* 3.1 36.2 + - + +
348B ARG* 5.3 5.2 + - - +
351B ALA* 3.9 4.2 - - + +
352B GLU* 3.6 26.8 + - - +
355B ALA* 3.8 21.0 - - + +
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Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B TYR* 2.9 42.1 + - + +
310B LEU* 4.0 4.0 - - + +
312B GLU* 1.3 77.1 - - - +
314B THR* 1.3 57.2 + - - +
316B LEU* 3.9 17.5 - - + +
317B GLY* 3.0 24.9 + - - -
404B LEU* 3.5 23.6 - - + -
407B GLN* 3.3 37.2 - - - +
411B ASN* 5.8 2.0 - - - +
436B VAL* 3.4 27.0 - - + +
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Residues in contact with THR 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B LEU 2.7 19.8 + - - -
311B ARG 2.9 8.4 + - - -
313B LEU* 1.3 75.4 - - - +
315B PHE* 1.3 61.6 + - + +
317B GLY* 3.1 1.4 + - - -
318B LEU* 2.9 32.3 + - + +
387B ALA* 4.4 14.6 - - + -
391B LEU* 3.7 18.2 - - + +
432B VAL* 3.7 29.8 - - + +
435B ALA* 3.8 18.6 - - + +
436B VAL* 3.6 15.1 - - - +
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Residues in contact with PHE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ARG* 3.1 39.1 + - + -
312B GLU* 3.9 0.9 - - - +
314B THR* 1.3 75.6 - - - +
316B LEU* 1.3 64.3 + - - +
317B GLY 3.3 0.2 + - - -
318B LEU* 4.8 6.3 - - + -
319B LEU* 3.6 6.4 + - - +
331B TYR* 2.8 37.7 + - + +
351B ALA* 3.9 25.8 - - + -
354B LEU* 3.8 48.9 - - + -
355B ALA 3.9 1.3 - - - -
362B TRP* 4.8 3.1 - + - -
384B LEU* 4.1 25.4 - - + -
387B ALA* 5.5 2.5 - - + -
388B LEU* 4.0 24.7 - - + -
391B LEU* 4.3 15.5 - - + -
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B TYR* 6.4 0.7 - - + -
312B GLU* 3.1 28.9 + - + +
313B LEU* 3.9 17.9 - - + +
315B PHE* 1.3 77.4 - - - +
317B GLY* 1.3 61.2 + - - +
319B LEU* 3.8 8.2 - - + +
320B ARG* 3.6 26.7 + - - +
347B GLU* 4.6 17.3 - - + +
348B ARG* 3.7 59.2 - - + +
351B ALA* 3.8 12.1 - - + -
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Residues in contact with GLY 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B LEU 3.0 14.5 + - - -
314B THR 3.1 4.0 + - - -
316B LEU* 1.3 76.6 - - - +
318B LEU* 1.3 59.5 + - - +
319B LEU 3.2 0.2 - - - -
320B ARG* 3.1 18.4 + - - +
321B ARG* 2.8 29.2 + - - +
435B ALA* 3.5 25.5 - - - +
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Residues in contact with LEU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B THR* 2.9 20.9 + - + +
315B PHE* 3.7 8.3 + - + -
316B LEU 3.5 0.2 - - - -
317B GLY* 1.3 74.5 - - - +
319B LEU* 1.3 56.7 + - - +
321B ARG* 2.8 4.5 + - - -
322B TYR* 2.7 63.4 + - + +
326B ILE* 4.2 14.8 - - + +
331B TYR* 3.6 17.0 - - - +
383B ILE* 3.7 20.6 - - + +
384B LEU* 5.0 5.4 - - + -
387B ALA* 3.8 24.2 - - + -
431B LEU* 4.1 11.9 - - + -
435B ALA* 4.1 17.2 - - + +
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B PHE 3.6 7.3 + - - +
316B LEU* 3.8 13.0 - - + +
317B GLY 3.2 0.4 - - - -
318B LEU* 1.3 79.2 - - - +
320B ARG* 1.3 59.6 + - - +
323B PRO* 4.1 14.7 - - + +
326B ILE* 3.7 27.2 - - - +
327B THR* 4.4 3.1 - - + -
328B GLU* 3.6 28.5 - - + +
331B TYR* 3.6 30.3 + - + -
347B GLU* 3.5 42.8 - - + +
350B LEU* 5.7 0.2 - - + -
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Residues in contact with ARG 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B LEU* 3.6 16.8 + - - +
317B GLY* 3.1 12.0 + - - +
319B LEU* 1.3 77.4 - - - +
321B ARG* 1.3 71.6 + - - +
323B PRO* 4.2 8.6 - - - +
347B GLU* 5.2 6.3 - - - +
411B ASN* 5.4 5.5 + - - +
435B ALA 3.8 20.2 + - - -
436B VAL* 4.7 10.1 + - - +
437B GLY* 4.8 4.0 - - - +
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Residues in contact with ARG 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B GLY 2.8 12.1 + - - +
318B LEU* 2.8 13.1 + - + +
320B ARG* 1.3 92.4 - - - +
322B TYR* 1.3 73.1 + - + +
323B PRO* 3.5 6.7 - - - +
434B TYR* 2.6 86.0 + - + -
435B ALA* 4.0 11.2 + - - +
437B GLY* 3.8 11.7 - - - +
439B THR 3.3 7.3 + - - -
440B ASN* 2.2 43.2 + - - +
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Residues in contact with TYR 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU* 2.7 47.9 + - + +
319B LEU 4.4 1.1 - - - -
321B ARG* 1.3 90.6 - - + +
323B PRO* 1.4 58.7 - - - +
324B ASP 3.2 2.8 + - - -
325B ARG* 3.6 41.3 - - + +
326B ILE* 2.8 35.5 + - + +
383B ILE* 3.8 17.9 - - + -
431B LEU* 3.4 18.5 - - + +
434B TYR* 3.4 15.5 - + - -
442B ASP* 2.7 41.7 + - - -
444B LEU* 3.5 10.3 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il